Biology subjects

Roldan, A.

Publications and source records attributed to Roldan, A..

12 recordsLinked to original sources

bioRxiv2026

Nationwide Spread of Fluconazole-Resistant Candida parapsilosis Clones: Insights from the Antifungal Resistance Surveillance Program

Background: Outbreaks of fluconazole-resistant Candida parapsilosis have recently emerged worldwide. In Spain, this phenomenon has been reported since 2020, mainly involving isolates from different clones harbouring the Y132F mutation at Erg11. Methods: We analysed the expansion of fluconazole resistant C. parapsilosis strains within the national antifungal resistance surveillance program. Genetic clustering and relationships were assessed using microsatellite typing and whole genome sequencing. Findings: We identified the expansion of three distinct clones carrying the Y132F mutation. Additionally, there was an increase in strains harbouring the G458S mutation, most of which belonged to a clonal complex, although other less prevalent clones were also detected. G458S isolates showed higher resistance to azoles than Y132F strains, particularly to voriconazole and isavuconazole. This increased resistance was associated with mutations in the Tac1 transcriptional regulator and duplication of a chromosomal region containing Tac1 and Erg11. One G458S isolate without mutation at Tac1 exhibited lower MIC values. Furthermore, two isolates carried the K143R mutation, and a distinct group of resistant strains without detectable ERG11 mutations was also identified. Resistant cases were detected across 31 hospitals in 12 autonomous regions. Interpretation: Our findings indicate a concerning nationwide expansion of antifungal-resistant C. parapsilosis in Spain, involving multiple resistance mechanisms and clonal lineages, with implications for antifungal treatment and infection control strategies.

microbiology↗

bioRxiv2026

Dissection of genotype-phenotype relationships in Candida parapsilosis uncovers drivers of clinically-relevant traits

Hospital outbreaks caused by the fungal pathogen Candida parapsilosis are of growing concern due to their increased drug resistance and high mortality rates. However, the genetic bases of clinically-relevant traits in this species remain poorly explored. Here, we mapped genotype-phenotype relationships across 189 isolates from a multi-hospital Candida parapsilosis outbreak, for which we measured 61 diverse clinical phenotypes and generated complete genome sequences. As variation in previously-known genes explained little of the observed phenotypic diversity, we leveraged convergence genome-wide association studies and interpretable machine-learning models that predict phenotypes from genetic variants. These approaches identified candidate drivers of virulence and antifungal resistance, confirming expected mechanisms while uncovering novel ones. Predictive models were accurate for key traits, including azole resistance and clinical features of infected patients. Our results shed light on the genetic bases of clinically-relevant traits in a major fungal pathogen, and pave the way towards sequence-based diagnostics for improved patient outcomes.

microbiology↗

bioRxiv2026

A plant single nucleotide polymorphism impacts nectar sugar composition, microbial diversity and pollinator visits

Nectar is a hub for plant-pollinator interactions, yet gene-level causal links between plant genetic variation, pollinator foraging and nectar microbial assembly remain poorly resolved. Using near-isogenic lines, innovative field time-lapse monitoring of pollinator visits and long-read amplicon sequencing of nectar microbiota, we show that a natural single-nucleotide variant at a cell-wall invertase gene (HaCWINV2) controls sunflower nectar chemistry and influences both pollinators and microbes. Plants homozygous for a loss-of-function HaCWINV2 allele produce sucrose-rich nectar, resulting in fewer bee visits under field conditions, while bumblebee visitation remained unaffected. In pollinator-excluded flowers, invertase-deficient plants harboured greater fungal diversity and compositionally distinct communities, indicating that nectar sugar profiles act as ecological filters shaping the nectar microbiome. This loss-of-function allele was found rarely and only at the heterozygote state in wild sunflowers and was fixed in 35% of cultivated lines indicating a positive selection during domestication. Our findings establish a causal link between a single gene and nectar chemistry with cascading ecological effects in a plant-pollinator system, illustrating how subtle genetic changes scale up to alter nectar traits, microbial assembly and pollinator foraging behaviour.

genetics↗

bioRxiv2026

BiOS: An Open-Source Framework for the Integration of Heterogeneous Biodiversity Data

The era of Big Data has reshaped biodiversity research, yet the potential of this information is frequently constrained by data heterogeneity, incompatible schemas, and the fragmentation of resources. Whilst standards such as Darwin Core have improved interoperability, significant barriers persist in harmonising multi-typology datasets ranging from taxonomy and genetics to species distribution. Here, we present the Biodiversity Observatory System (BiOS), a comprehensive, open-source software stack designed to address these impediments through a modular, community-driven architecture. BiOS departs from monolithic database designs by decoupling the back-end data management from the front-end presentation layer. This architectural separation supports a dual-access model tailored to diverse stakeholder needs. For researchers and developers, the system offers a comprehensive Application Programming Interface (API) that exposes all back-end functionalities, enabling seamless programmatic access, automated data retrieval, and integration with external analytical workflows. Simultaneously, the platform features a user web interface designed to lower the technical barrier to entry. This interface facilitates intuitive data exploration through agile taxonomic navigation, advanced geospatial map viewers for species occurrence filtering, and dedicated dashboards for visualising genetic markers and legislative status. Strictly adhering to the FAIR principles (Findable, Accessible, Interoperable, Reusable), BiOS acts as a relational engine capable of integrating heterogeneous data streams. By providing a flexible, interoperable core that supports the "seven shortfalls" framework of biodiversity knowledge, BiOS offers a turnkey solution to overcome data fragmentation and enhance collaborative conservation efforts.

bioinformatics↗

bioRxiv2025

Specifind: A Natural Language Processing Tool for Automating Species Occurrence (Re-)Discovery from Scientific Literature

A vast amount of valuable information on species occurrences remains embedded within the unstructured and continuously expanding body of ecological literature written in natural language. When effectively extracted, such dispersed knowledge has the potential to significantly improve understanding of species distributions and ecological patterns, thereby enabling more targeted and informed conservation actions. To address this challenge, Specifind is introduced as a tool designed to facilitate the extraction of species occurrence data through the identification of scientific species names, geographic references, and the relationships between them while ensuring traceability. At its core lies a newly developed and expertly annotated dataset comprising over one thousand open-access abstracts drawn from five domains: biogeography, botany, entomology, mycology, and zoology. A suite of Natural Language Processing components has been integrated, including Document Layout Analysis, Optical Character Recognition, Named Entity Recognition, Coreference Resolution, and Relation Extraction. These components enable the accurate identification and contextual linking of species and geographic entities, even when references are distributed throughout the text. As a result, Specifind enhances the discoverability and usability of species occurrence information embedded within unstructured scientific texts. It is expected to reduce the substantial effort required for manual literature review, thereby supporting biodiversity research, informing conservation planning, and facilitating ecological analysis.

bioinformatics↗

bioRxiv2025

Multilayered human activities shape the microbial communities of groundwater-dependent ecosystems in an arid oceanic island

Island coastal aquifers, though physically small compared to continental groundwater systems, are of huge ecological and societal importance, sustaining functions that connect to locally crucial provision, maintenance and culture ecosystem services. Those functions are largely dependent on the presence of highly adapted biological communities, for which, their microbial communities remain understudied. Our goal is to describe the bacterial communities across the groundwater-dependent ecosystems on Lanzarote, spanning a gradient of anthropogenic pollution using 16SrRNA amplicon sequencing. We sampled coastal caves and pools, wells and water galleries, springs, saltworks and marine bays affected by submarine groundwater discharge. Ecological analyses highlight that richness and composition of bacterial communities strongly depend on the type of habitats. Pathogens and human-derived species were ubiquitous in our samples, but, strikingly, caves and wells were strongly enriched with them compared to other habitats. We propose that our results highlight the susceptibility of groundwater environments to pollution and indicate that aquifers act as reservoirs of biological contamination in addition to natural diversity--regardless of their salinity. Since this enrichment might compromise some of the functions and services that groundwater-dependent ecosystems provide in oceanic islands, we call for integrative conservation strategies that include hydrological and biological perspectives into the decision making.

microbiology↗

bioRxiv2025

biodumpy: A Comprehensive Biological Data Downloader

In recent years, the expansion of public biodiversity platforms and associated datasets has greatly improved access to ecological and biological information. These resources now cover vast geographic areas, extended temporal scales, and diverse taxonomic groups, becoming essential for ecological studies by enabling more comprehensive analyses and novel hypotheses testing. Concurrently, the development of programming packages has facilitated data access and interaction, streamlining their retrieval processes. However, most existing tools are limited to specific databases, posing challenges for studies requiring seamless integration of data from multiple sources. The growing availability of biodiversity data highlights the urgent need for robust tools to efficiently process, analyse, and interpret ecological and biological information. To address this limitation, we introduce biodumpy, a new Python package developed for the retrieval, management, and integration of biological data from various public databases. biodumpy provides access to up-to-date and comprehensive datasets spanning genetic, distributional, taxonomic, and bibliographic sources. It includes specialized modules for efficient data retrieval across taxonomic lists, with the capability to process multiple modules simultaneously. By integrating diverse data sources, biodumpy enhances data acquisition, providing researchers with a powerful framework for comprehensive analyses and supporting ecological research to tackle complex environmental challenges.

ecology↗

bioRxiv2024

Deleterious imprinting of perinatal exposure to nano-polystyrene on inflammatory bowel diseases

The tremendous and exponential production of plastics as well as its poor recycling leads to massive release in the environment questioning their outcomes on human health. Plastics are degraded into micro-plastic (MPL) and nano-plastic (NPL) that undergo weathering. MPL and NPL enter the human food chain via contaminated food, when animals are bred or vegetables grew on in plastic polluted environment and through the degradation of plastics food packaging. Ingested MPL or NPL can pass through epithelial barrier. This study focuses on consequences of oral perinatal exposure to polystyrene 50nm pristine or weathered (w) on intestinal disorders onset in offspring. Mouse were forced fed daily with 1.25mg of PS50 or PS50w starting at 15 days of gestation until pups weaned (Post Natal Day PND21). Oral tolerance protocol was induced at PND15 (nutritional switch) with ovalbumin (OVA) whereas DSS-induced colitis was performed in PND63 offspring. PS50 nor PS50w perinatal exposure did impair tolerance or immunization to OVA at PND15 in male or females. However, PS50 and PS50w perinatal exposure significantly worsened macroscopic score of DSS-induced colitis in both sexes. Perinatal exposure to PS50w appeared to be even more deleterious than PS50 for colitis exacerbation in males. In conclusion, early life exposure to PS50 or PS50w has long-lasting consequences on gut physiology by increasing the colonic severity of colitis while it does not modify oral tolerance establishment in early life. Those preliminary results questioned the kinetic of perinatal PS50 and PS50w exposure outcome over the life course and introduce the notion of imprinting. HighlightsO_LIPerinatal exposure to PS50 or PS50w does not affect oral tolerance establishment nor immune response to immunisation at PND15 C_LIO_LIPerinatal exposure to PS50 or PS50w have long lasting consequences on intestinal inflammation and colitis. PS50w in male has even more deleterious outcomes. C_LIO_LIRestricted exposure to PS50 or PS50w during perinatal has a deleterious imprinting on adult offspring intestinal health C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/629591v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@13bae52org.highwire.dtl.DTLVardef@131b42eorg.highwire.dtl.DTLVardef@2c7317org.highwire.dtl.DTLVardef@380df8_HPS_FORMAT_FIGEXP M_FIG C_FIG Environmental implicationThe use of plastics in daily products leads to ubiquitous contamination of the environment and subsequently of food chains. Plastics persist for long periods in the environment where, submitted to climate, they fragment into nanoplastic particles (NPL). Indeed, these NPL are weathered due to their exposure to UV light, thermal, chemical, physical and biological stresses. Thus, human populations are exposed to pristine (NPLp) and weathered NPL (NPLw) in their daily lives, with unknown effect on intestinal health, including the diseases development like adverse Food Reactions (AFR) or Inflammatory Bowel Diseases (IBD). Given that these pathologies could originate in perinatal development and that pregnant and breastfeeding women are exposed to NPL on a daily basis, this study explores the impact of perinatally exposure to pristine or weathered polystyrene nanoplastics on the gut development and susceptibility.

pathology↗

bioRxiv2023

Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling

AbstractThe folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR post-translational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their post-translational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding. One-Sentence SummaryAllosteric interdomain communication and its modulation are critical determinants of ABCC-transporters post-translational conformational biogenesis, misfolding, and pharmacological rescue.

biophysics↗

bioRxiv2022

Robust Harmonization of Microbiome Studies by Phylogenetic Scaffolding with MaLiAmPi

Microbiome science is difficult to translate back to patients due to an inability to harmonize 16S rRNA gene-based microbiome data, as differences in the technique will result in different amplicon sequence variants (ASV) from the same microbe. Here we demonstrate that placement of ASV onto a common phylogenetic tree of full-length 16S rRNA alleles can harmonize microbiome studies. Using in silico data approximating 100 healthy human stool microbiomes we demonstrated that phylogenetic placement of ASV can recapitulate the true relationships between communities as compared closed-OTU based approaches (Spearman R 0.8 vs 0.2). Using real data from thousands of human gut and vaginal microbiota, we demonstrate phylogenetic placement, but not closed OTUs, were able to group communities by origin (stool vs vaginal) without being confounded by technique and integrate new data into existing ordination/clustering models for precision medicine. This enables meta-analysis of microbiome studies and the microbiome as a biomarker.

bioinformatics↗

bioRxiv2022

Aspergillus fumigatus can exhibit persistence to the fungicidal drug voriconazole

Aspergillus fumigatus is a filamentous fungus that can infect the lungs of patients with immunosuppression and/or underlying lung-diseases. The mortality associated with chronic and invasive aspergillosis infections remain very high, despite availability of antifungal treatments. In the last decade, there has been a worrisome emergence and spread of resistance to the first line antifungals, the azoles. The mortality caused by resistant isolates is even higher, and patient management is complicated as the therapeutic options are reduced. Nevertheless, treatment failure is also common in patients infected with azole-susceptible isolates, which can be due to several non- mutually exclusive reasons, such as poor drug absorption. In addition, the phenomena of tolerance or persistence, where susceptible pathogens can survive the action of an antimicrobial for extended periods, have been associated with treatment failure in bacterial infections, and their occurrence in fungal infections already proposed. Here, we demonstrate that some isolates of A. fumigatus display persistence to voriconazole. A sub-population of the persister isolates can survive for extended periods and even grow at slow rates in the presence of supra-MIC (Minimum Inhibitory Concentration) of voriconazole and seemingly other azoles. Persistence cannot be eradicated with adjuvant drugs or antifungal combinations and seems to reduce the efficacy of treatment for certain individuals in a Galleria mellonella model of infection. Furthermore, persistence implies a distinct transcriptional profile, demonstrating that it is an active response. We propose that azole persistence might be a relevant and underestimated factor that could influence the outcome of infection in human aspergillosis. IMPORTANCEThe phenomena of antibacterial tolerance and persistence, where pathogenic microbes can survive for extended periods in the presence of cidal drug concentrations, have received significant attention in the last decade. Several mechanisms of action have been elucidated, and their relevance for treatment failure in bacterial infections demonstrated. In contrast, our knowledge about antifungal tolerance and, particularly, persistence are still very scarce. In this study, we have characterised the response of the prominent fungal pathogen Aspergillus fumigatus to the first line therapy antifungal voriconazole. We comprehensively show that some isolates display persistence to this fungicidal antifungal and identify various potential mechanisms of action. In addition, using an alternative model of infection, we provide initial evidence to suggest that persistence may cause treatment failure in some individuals. Therefore, we propose that azole persistence is an important factor to consider and further investigate in A. fumigatus.

microbiology↗

bioRxiv2018

Host identity and functional traits determine the community composition of the arbuscular mycorrhizal fungi in facultative epiphytic plant species

The epiphytic vascular flora is scarce and facultative in semiarid Mediterranean ecosystems, thus covering diverse taxonomic groups. However, differently to terrestrial conditions, little is known about the factors driving mycorrhizal communities in epiphytic environments. Here, we investigated the arbuscular mycorrhizal fungi (AMF) harboured by 31 plant species occurring in the trunks of Phoenix dactylifera. We wanted to ascertain if host identity and plant functional traits shape mycorrhizal communities. Specifically, we tested the plant life-cycle (perennial versus annual), the plant life-form (herbaceous versus woody), the plant origin (exotic versus native) and the plant species.\n\nThe roots were examined by molecular and phylogenetic analysis of AMF community. The plant affiliation to species strongly influenced the AMF assemblages. Plant life-form and plant life-cycle also shaped AMF interactions. The AMF community differed between annual and perennial species and higher AMF richness was detected in perennial plants. The indicator species analysis revealed three Operational Taxonomic Units belonging to the Glomeraceae, associated with annual species. However, the epiphytic plants associated with AMF irrespective of whether they were native or not, probably because here no functional differences derive from plant origin.\n\nIMPORTANCEArbuscular mycorrhizal (AM) symbiosis has a decisive role in plant nutrient and water uptake by plants, with particular importance in stressful environments. Under semiarid conditions, the facultative epiphytic flora should cope with harsh conditions. While numerous studies have been conducted on factors driving terrestrial AM assemblages, the epiphytic environment remains unexplored. We offer new insights into composition of AM communities as shaped by epiphytic plant host identity and functional traits.

microbiology↗